# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 22:15:46 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2S,5R,6R)-3,3-dimethyl-7-oxo-6-[(phenoxyacetyl)amino]-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H]2[C@H](NC(=O)COc3ccccc3)C(=O)N2[C@H]1C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PNV  PNV  '(2S,5R,6R)-3,3-dimethyl-7-oxo-6-[(phenoxyacetyl)amino]-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  42  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNV
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PNV  C24  C  CR16  0  -0.344   6.3385   0.7600  -0.6338
 PNV  C23  C  CR16  0  -0.240   7.6001   0.2088  -0.4975
 PNV  C22  C  CR16  0  -0.280   7.7675  -1.0419   0.0895
 PNV  C21  C  CR16  0  -0.241   6.6523  -1.7301   0.5380
 PNV  C20  C  CR16  0  -0.376   5.3764  -1.1889   0.4112
 PNV  C19  C  CR6   0   0.384   5.2187   0.0621  -0.1782
 PNV  O1   O  O2    0  -0.465   4.0289   0.6798  -0.3511
 PNV  C2   C  CH2   0  -0.309   2.8713   0.0280   0.0858
 PNV  C3   C  C     0   0.526   1.6880   0.9190  -0.2446
 PNV  O18  O  O     0  -0.454   1.7924   1.9567  -0.8625
 PNV  N4   N  NH1   0  -0.645   0.5136   0.4269   0.2158
 PNV  C5   C  C     0  -0.230  -0.7247   1.0936   0.0366
 PNV  C6   C  C     0   0.524  -1.7012   1.0851   1.2207
 PNV  O17  O  O     0  -0.396  -1.6251   1.2518   2.4049
 PNV  C8   C  C     0  -0.207  -1.8847   0.3998  -0.7187
 PNV  N7   N  N     0  -0.419  -2.7498   0.7098   0.4147
 PNV  S11  S  S2    0   0.071  -1.8578  -1.4082  -0.7448
 PNV  C10  C  CT    0  -0.260  -3.6425  -1.4331  -0.2620
 PNV  C12  C  CH3   0  -0.644  -4.4943  -1.2055  -1.5081
 PNV  C15  C  CH3   0  -0.637  -3.9587  -2.7804   0.3680
 PNV  C9   C  CH1   0  -0.149  -3.7598  -0.2566   0.7681
 PNV  C13  C  C     0   0.547  -5.1427   0.3669   0.7801
 PNV  O14  O  OH1   0  -0.583  -6.0129  -0.4259   1.3856
 PNV  O16  O  O     0  -0.417  -5.4109   1.4352   0.3019
 PNV  H1   H  HCR6  0   0.264   6.2086   1.7321  -1.0934
 PNV  H2   H  HCR6  0   0.259   8.4605   0.7618  -0.8519
 PNV  H3   H  HCR6  0   0.254   8.7553  -1.4695   0.1963
 PNV  H4   H  HCR6  0   0.260   6.7644  -2.7031   0.9986
 PNV  H5   H  HCR6  0   0.282   4.5293  -1.7558   0.7736
 PNV  H6   H  HCH2  0   0.270   2.7349  -0.9415  -0.4107
 PNV  H7   H  HCH2  0   0.269   2.8916  -0.1618   1.1661
 PNV  H8   H  HNH1  0   0.416   0.5167  -0.4451   0.7247
 PNV  H9   H  H     0   0.335  -0.5489   2.1002  -0.3439
 PNV  H10  H  H     0   0.308  -2.1819   0.8318  -1.6730
 PNV  H11  H  HCH3  0   0.263  -4.2902  -1.9848  -2.2406
 PNV  H12  H  HCH3  0   0.248  -5.5590  -1.2588  -1.2707
 PNV  H13  H  HCH3  0   0.253  -4.3002  -0.2419  -1.9794
 PNV  H14  H  HCH3  0   0.251  -3.3356  -2.9774   1.2399
 PNV  H15  H  HCH3  0   0.255  -5.0032  -2.8170   0.6767
 PNV  H16  H  HCH3  0   0.254  -3.8040  -3.5831  -0.3534
 PNV  H17  H  HCH1  0   0.314  -3.5454  -0.6425   1.7702
 PNV  H18  H  HOH1  0   0.490  -6.9007  -0.0363   1.3609

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PNV  C22  C21  aromatic  1.385  0.020  1.385
 PNV  C22  C23  aromatic  1.392  0.020  1.392
 PNV  C21  C20  aromatic  1.392  0.020  1.392
 PNV  C23  C24  aromatic  1.383  0.020  1.383
 PNV  C20  C19  aromatic  1.392  0.020  1.392
 PNV  C24  C19  aromatic  1.396  0.020  1.396
 PNV  C19  O1   single    1.352  0.020  1.352
 PNV  O1   C2   single    1.398  0.020  1.398
 PNV  C2   C3   single    1.518  0.020  1.518
 PNV  C3   N4   single    1.354  0.020  1.354
 PNV  C3   O18  double    1.212  0.020  1.212
 PNV  N4   C5   single    1.418  0.020  1.418
 PNV  C5   C6   single    1.535  0.020  1.535
 PNV  C5   C8   single    1.548  0.020  1.548
 PNV  O17  C6   double    1.198  0.020  1.198
 PNV  C6   N7   single    1.375  0.020  1.375
 PNV  C8   N7   single    1.459  0.020  1.459
 PNV  C8   S11  single    1.808  0.020  1.808
 PNV  N7   C9   single    1.442  0.020  1.442
 PNV  S11  C10  single    1.849  0.020  1.849
 PNV  C9   C10  single    1.568  0.020  1.568
 PNV  C9   C13  single    1.517  0.020  1.517
 PNV  C10  C15  single    1.521  0.020  1.521
 PNV  C10  C12  single    1.527  0.020  1.527
 PNV  C13  O16  double    1.201  0.020  1.201
 PNV  C13  O14  single    1.324  0.020  1.324
 PNV  C24  H1   single    0.930  0.020  1.080
 PNV  C23  H2   single    0.930  0.020  1.080
 PNV  C22  H3   single    0.930  0.020  1.080
 PNV  C21  H4   single    0.930  0.020  1.080
 PNV  C20  H5   single    0.930  0.020  1.080
 PNV  C2   H6   single    0.970  0.020  1.090
 PNV  C2   H7   single    0.970  0.020  1.090
 PNV  N4   H8   single    0.860  0.020  1.020
 PNV  C5   H9   single    0.970  0.020  1.090
 PNV  C8   H10  single    0.970  0.020  1.090
 PNV  C12  H11  single    0.970  0.020  1.090
 PNV  C12  H12  single    0.970  0.020  1.090
 PNV  C12  H13  single    0.970  0.020  1.090
 PNV  C15  H14  single    0.970  0.020  1.090
 PNV  C15  H15  single    0.970  0.020  1.090
 PNV  C15  H16  single    0.970  0.020  1.090
 PNV  C9   H17  single    0.970  0.020  1.090
 PNV  O14  H18  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PNV  H1   C24  C19  119.41  3.000
 PNV  H1   C24  C23  120.58  3.000
 PNV  C19  C24  C23  120.01  3.000
 PNV  H2   C23  C22  120.10  3.000
 PNV  H2   C23  C24  119.28  3.000
 PNV  C22  C23  C24  120.62  3.000
 PNV  H3   C22  C21  120.45  3.000
 PNV  H3   C22  C23  120.45  3.000
 PNV  C21  C22  C23  119.09  3.000
 PNV  H4   C21  C20  118.90  3.000
 PNV  H4   C21  C22  120.07  3.000
 PNV  C20  C21  C22  121.03  3.000
 PNV  H5   C20  C19  121.61  3.000
 PNV  H5   C20  C21  118.92  3.000
 PNV  C19  C20  C21  119.47  3.000
 PNV  O1   C19  C20  124.37  3.000
 PNV  O1   C19  C24  115.84  3.000
 PNV  C20  C19  C24  119.78  3.000
 PNV  C2   O1   C19  118.41  3.000
 PNV  H7   C2   H6   107.15  3.000
 PNV  H7   C2   C3   109.29  3.000
 PNV  H6   C2   C3   108.85  3.000
 PNV  H7   C2   O1   111.90  3.000
 PNV  H6   C2   O1   111.91  3.000
 PNV  C3   C2   O1   107.69  3.000
 PNV  N4   C3   O18  124.00  3.000
 PNV  O18  C3   C2   123.11  3.000
 PNV  N4   C3   C2   112.89  3.000
 PNV  H8   N4   C5   118.20  3.000
 PNV  H8   N4   C3   118.86  3.000
 PNV  C5   N4   C3   122.94  3.000
 PNV  H9   C5   C8   111.36  3.000
 PNV  H9   C5   C6   112.15  3.000
 PNV  C8   C5   C6    84.10  3.000
 PNV  H9   C5   N4   109.71  3.000
 PNV  C8   C5   N4   120.35  3.000
 PNV  C6   C5   N4   117.10  3.000
 PNV  N7   C6   O17  131.74  3.000
 PNV  N7   C6   C5    91.98  3.000
 PNV  O17  C6   C5   136.16  3.000
 PNV  H10  C8   S11  112.84  3.000
 PNV  H10  C8   N7   115.76  3.000
 PNV  S11  C8   N7   103.44  3.000
 PNV  H10  C8   C5   117.01  3.000
 PNV  S11  C8   C5   116.35  3.000
 PNV  N7   C8   C5    88.28  3.000
 PNV  C9   N7   C8   117.60  3.000
 PNV  C9   N7   C6   125.00  3.000
 PNV  C8   N7   C6    93.51  3.000
 PNV  C10  S11  C8    89.73  3.000
 PNV  C9   C10  C15  112.15  3.000
 PNV  C15  C10  C12  110.75  3.000
 PNV  C9   C10  C12  112.49  3.000
 PNV  C12  C10  S11  108.87  3.000
 PNV  C15  C10  S11  108.72  3.000
 PNV  C9   C10  S11  103.51  3.000
 PNV  H13  C12  H12  108.10  3.000
 PNV  H13  C12  H11  107.97  3.000
 PNV  H12  C12  H11  107.10  3.000
 PNV  H13  C12  C10  112.67  3.000
 PNV  H12  C12  C10  111.05  3.000
 PNV  H11  C12  C10  109.74  3.000
 PNV  H16  C15  H15  107.38  3.000
 PNV  H16  C15  H14  108.38  3.000
 PNV  H15  C15  H14  108.38  3.000
 PNV  H16  C15  C10  110.41  3.000
 PNV  H15  C15  C10  110.27  3.000
 PNV  H14  C15  C10  111.88  3.000
 PNV  H17  C9   C13  108.42  3.000
 PNV  H17  C9   C10  108.79  3.000
 PNV  C13  C9   C10  112.44  3.000
 PNV  H17  C9   N7   108.87  3.000
 PNV  C13  C9   N7   111.41  3.000
 PNV  C10  C9   N7   106.83  3.000
 PNV  O16  C13  O14  124.62  3.000
 PNV  O14  C13  C9   110.90  3.000
 PNV  O16  C13  C9   124.48  3.000
 PNV  H18  O14  C13  110.46  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PNV  CONST_01  C21  C22  C23  C24     0.00   0.0  0
 PNV  CONST_02  C21  C20  C19  C24     0.00   0.0  0
 PNV  CONST_03  C20  C21  C22  C23     0.00   0.0  0
 PNV  CONST_04  C20  C19  C24  C23     0.00   0.0  0
 PNV  CONST_05  C19  C20  C21  C22     0.00   0.0  0
 PNV  CONST_06  C19  C24  C23  C22     0.00   0.0  0
 PNV  CONST_07  C8   N7   C6   C5      0.00   0.0  0
 PNV  CONST_09  O1   C19  C24  C23   180.00   0.0  0
 PNV  CONST_10  O1   C19  C20  C21   180.00   0.0  0
 PNV  CONST_13  H3   C22  C23  C24   180.00   0.0  0
 PNV  CONST_14  H5   C20  C19  C24   180.00   0.0  0
 PNV  CONST_15  H4   C21  C22  C23   180.00   0.0  0
 PNV  CONST_16  H1   C24  C23  C22   180.00   0.0  0
 PNV  CONST_17  H2   C23  C22  C21   180.00   0.0  0
 PNV  CONST_18  C5   N4   C3   C2    180.00   0.0  0
 PNV  CONST_19  C5   N4   C3   O18     0.00   0.0  0
 PNV  CONST_20  H18  O14  C13  C9    180.00   0.0  0
 PNV  CONST_21  H8   N4   C3   C2      0.00   0.0  0
 PNV  Var_01    C9   C10  S11  C8    -38.63  30.0  1
 PNV  Var_02    H14  C15  C10  S11    58.43  30.0  3
 PNV  Var_03    H11  C12  C10  S11    59.19  30.0  3
 PNV  Var_04    C3   C2   O1   C19  -179.11  30.0  3
 PNV  Var_05    N4   C3   C2   O1   -175.83  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PNV  chir_01  C5  N4   C6   C8   positiv
 PNV  chir_02  C8  S11  N7   C5   negativ
 PNV  chir_03  C9  N7   C10  C13  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PNV  plan-1  C24  0.020
 PNV  plan-1  C23  0.020
 PNV  plan-1  C22  0.020
 PNV  plan-1  C21  0.020
 PNV  plan-1  C20  0.020
 PNV  plan-1  C19  0.020
 PNV  plan-1  O1   0.020
 PNV  plan-1  H1   0.020
 PNV  plan-1  H2   0.020
 PNV  plan-1  H3   0.020
 PNV  plan-1  H4   0.020
 PNV  plan-1  H5   0.020
 PNV  plan-2  C2   0.020
 PNV  plan-2  C3   0.020
 PNV  plan-2  O18  0.020
 PNV  plan-2  N4   0.020
 PNV  plan-2  C5   0.020
 PNV  plan-2  H8   0.020
 PNV  plan-3  C5   0.020
 PNV  plan-3  C6   0.020
 PNV  plan-3  O17  0.020
 PNV  plan-3  C8   0.020
 PNV  plan-3  N7   0.020
 PNV  plan-3  C9   0.020
 PNV  plan-4  C9   0.020
 PNV  plan-4  C13  0.020
 PNV  plan-4  O14  0.020
 PNV  plan-4  O16  0.020
 PNV  plan-4  H18  0.020

